Browsing by Subject "Species distribution modeling"

Antillean manatees (Trichechus manatus manatus) were heavily hunted in the past throughout the Wider Caribbean Region (WCR), and are currently listed as endangered on the IUCN Red List of Threatened Species. In most WCR countries, including Haiti and the Dominican Republic, remaining manatee populations are believed to be small and declining, but current information is needed on their status, distribution, and local threats to the species.

To assess the past and current distribution and conservation status of the Antillean manatee in Hispaniola, I conducted a systematic review of documentary archives dating from the pre-Columbian era to 2013. I then surveyed more than 670 artisanal fishers from Haiti and the Dominican Republic in 2013-2014 using a standardized questionnaire. Finally, to identify important areas for manatees in the Dominican Republic, I developed a country-wide ensemble model of manatee distribution, and compared modeled hotspots with those identified by fishers.

Manatees were historically abundant in Hispaniola, but were hunted for their meat and became relatively rare by the end of the 19th century. The use of manatee body parts diversified with time to include their oil, skin, and bones. Traditional uses for folk medicine and handcrafts persist today in coastal communities in the Dominican Republic. Most threats to Antillean manatees in Hispaniola are anthropogenic in nature, and most mortality is caused by fisheries. I estimated a minimum island-wide annual mortality of approximately 20 animals. To understand the impact of this level of mortality, and to provide a baseline for measuring the success of future conservation actions, the Dominican Republic and Haiti should work together to obtain a reliable estimate of the current population size of manatees in Hispaniola.

In Haiti, the survey of fishers showed a wider distribution range of the species than suggested by the documentary archive review: fishers reported recent manatee sightings in seven of nine coastal departments, and three manatee hotspot areas were identified in the north, central, and south coasts. Thus, the contracted manatee distribution range suggested by the documentary archive review likely reflects a lack of research in Haiti. Both the review and the interviews agreed that manatees no longer occupy freshwater habitats in the country. In general, more dedicated manatee studies are needed in Haiti, employing aerial, land, or boat surveys.

In the Dominican Republic, the documentary archive review and the survey of fishers showed that manatees still occur throughout the country, and occasionally occupy freshwater habitats. Monte Cristi province in the north coast, and Barahona province in the south coast, were identified as focal areas. Sighting reports of manatees decreased from Monte Cristi eastwards to the adjacent province in the Dominican Republic, and westwards into Haiti. Along the north coast of Haiti, the number of manatee sighting and capture reports decreased with increasing distance to Monte Cristi province. There was good agreement among the modeled manatee hotspots, hotspots identified by fishers, and hotspots identified during previous dedicated manatee studies. The concordance of these results suggests that the distribution and patterns of habitat use of manatees in the Dominican Republic have not changed dramatically in over 30 years, and that the remaining manatees exhibit some degree of site fidelity. The ensemble modeling approach used in the present study produced accurate and detailed maps of manatee distribution with minimum data requirements. This modeling strategy is replicable and readily transferable to other countries in the Caribbean or elsewhere with limited data on a species of interest.

The intrinsic value of manatees was stronger for artisanal fishers in the Dominican Republic than in Haiti, and most Dominican fishers showed a positive attitude towards manatee conservation. The Dominican Republic is an upper middle income country with a high Human Development Index. It possesses a legal framework that specifically protects manatees, and has a greater number of marine protected areas, more dedicated manatee studies, and more manatee education and awareness campaigns than Haiti. The constant presence of manatees in specific coastal segments of the Dominican Republic, the perceived decline in the number of manatee captures, and a more conservation-minded public, offer hope for manatee conservation, as non-consumptive uses of manatees become more popular. I recommend a series of conservation actions in the Dominican Republic, including: reducing risks to manatees from harmful fishing gear and watercraft at confirmed manatee hotspots; providing alternative economic alternatives for displaced fishers, and developing responsible ecotourism ventures for manatee watching; improving law enforcement to reduce fisheries-related manatee deaths, stop the illegal trade in manatee body parts, and better protect manatee habitat; and continuing education and awareness campaigns for coastal communities near manatee hotspots.

In contrast, most fishers in Haiti continue to value manatees as a source of food and income, and showed a generally negative attitude towards manatee conservation. Haiti is a low income country with a low Human Development Index. Only a single dedicated manatee study has been conducted in Haiti, and manatees are not officially protected. Positive initiatives for manatees in Haiti include: protected areas declared in 2013 and 2014 that enclose two of the manatee hotspots identified in the present study; and local organizations that are currently working on coastal and marine environmental issues, including research and education on marine mammals. Future conservation efforts for manatees in Haiti should focus on addressing poverty and providing viable economic alternatives for coastal communities. I recommend a community partnership approach for manatee conservation, paired with education and awareness campaigns to inform coastal communities about the conservation situation of manatees in Haiti, and to help change their perceived value. Haiti should also provide legal protection for manatees and their habitat.

This dissertation focuses on solving some common problems associated with ecological field studies. In the core of the statistical methodology, lies spatial modeling that provides greater flexibility and improved predictive performance over existing algorithms. The applications involve prevalence datasets for hundreds of plants over a large area in the Cape Floristic Region (CFR) of South Africa.

In Chapter 2, we begin with modeling the categorical abundance data with a multi level spatial model using background information such as environmental and soil-type factors. The empirical pattern is formulated as a degraded version of the potential pattern, with the degradation effect accomplished in two stages. First, we adjust for land use transformation and then we adjust for measurement error, hence misclassification error, to yield the observed abundance classifications. With data on a regular grid over CFR, the analysis is done with a conditionally autoregressive prior on spatial random effects. With around ~ 37000 cells to work with, a novel paralleilization algorithm is developed for updating the spatial parameters to efficiently estimate potential and transformed abundance surfaces over the entire region.

In Chapter 3, we focus on a different but increasingly common type of prevalence data in the so called presence-only setting. We detail the limitations associated with a usual presence-absence analysis for this data and advocate modeling the data as a point pattern realization. The underlying intensity surface is modeled with a point-level spatial Gaussian process prior, after taking into account sampling bias and change in land-use pattern. The large size of the region enforces using an computational approximation with a bias-corrected predictive process. We compare our methodology against the the most commonly used maximum entropy method, to highlight the improvement in predictive performance.

In Chapter 4, we develop a novel hierarchical model for analyzing noisy point pattern datasets, that arise commonly in ecological surveys due to multiple sources of bias, as discussed in previous chapters. The effect of the noise leads to displacements of locations as well as potential loss of points inside a bounded domain. Depending on the assumption on existence of locations outside the boundary, a couple of different models -- island and subregion, are specified. The methodology assumes informative knowledge of the scale of measurement error, either pre-specified or learned from a training sample. Its performance is tested against different scales of measurement error related to the data collection techniques in CFR.

In Chapter 5, we suggest an alternative model for prevalence data, different from the one in Chapter 3, to avoid numerical approximation and subsequent computational complexities for a large region. A mixture model, similar to the one in Chapter 4 is used, with potential dependence among the weights and locations of components. The covariates as well as a spatial process are used to model the dependence. A novel birth-death algorithm for the number of components in the mixture is under construction.

Lastly, in Chapter 6, we proceed to joint modeling of multiple-species datasets. The challenge is to infer about inter-species competition with a large number of populations, possibly running into several hundreds. Our contribution involves applying hierarchical Dirichlet process to cluster the presence localities and subsequently developing measures of range overlap from posterior draws. This kind of simultaneous inference can potentially have implications for questions related to biodiversity and conservation studies. .

Open‐ocean fisheries expanded rapidly from the 1960s and currently represent the largest direct stressor on high seas biodiversity and ecosystems. Open-ocean ecological research and the implementation of management actions to mitigate the impacts of fisheries has lagged behind those of coastal and deep-sea environments. I investigate opportunities to enhance a wholistic ecosystem-based approach to high seas fisheries management by: reviewing our understanding of the impacts fisheries across ecological scales, evaluating the gaps and opportunities in the mandates of existing and future governance frameworks and developing methodologies for creating dynamic spatiotemporal management tools to reduce bycatch. Results demonstrate that fisheries are impacting the open-ocean across ecological scales. Results also show that the population trajectories of most non-target species in the high seas are not being monitored by fishing nations, nor relevant fisheries management organizations. A new implementing agreement under the UN to sustainably manage high seas biodiversity could complement the mandates fisheries bodies. There is an opportunity for new technologies and modeling approaches to contribute to the implementation of an ecosystem-based approach to management by generating knowledge on the spatial ecology commercial fisheries and high seas biodiversity. My results show that the distribution of target and non-target species, as well as longline fishing activities are correlated with environmental conditions and that these can be predicted across spatial and temporal scales to inform spatial management of high seas pelagic fishing activities. Implementing an ecosystem-based approach will require embracing a precautionary approach to reduce the bycatch of non-target species, which can be accomplished through spatiotemporal avoidance and improving our monitoring of fisheries impacts across ecological scales.